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r533: added --no-pairing

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to prevent the use of any pairing information for paired-end reads.
This commit is contained in:
Heng Li
2017-10-23 14:09:32 -04:00
parent 5acd709524
commit d4b5dfc297
3 changed files with 10 additions and 2 deletions
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main.c
+3 -1
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.3-r531"
#define MM_VERSION "2.3-r533-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -41,6 +41,7 @@ static struct option long_options[] = {
{ "secondary", optional_argument, 0, 0 },
{ "cs", optional_argument, 0, 0 },
{ "end-bonus", required_argument, 0, 0 },
{ "no-pairing", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -135,6 +136,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==17) opt.end_bonus = atoi(optarg); // --end-bonus
else if (c == 0 && long_idx ==18) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
else if (c == 0 && long_idx == 14) { // --frag
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_FRAG_MODE;